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Cladistics and the Origin of Birds: a Review and Two New Analyses Cladistics and the Origin of Birds: A Review and Two New Analyses OM66_FM.indd 1 3/31/09 4:56:43 PM Ornithological Monographs Editor: John Faaborg 224 Tucker Hall Division of Biological Sciences University of Missouri Columbia, Missouri 65211 Managing Editor: Mark C. Penrose Copy Editor: Richard D. Earles Authors of this issue: Frances C. James and John A. Pourtless IV Translation of the abstract by Lisbeth O. Swain The Ornithological Monographs series, published by the American Ornithologists’ Union, has been established for major papers and presentations too long for inclusion in the Union’s journal, The Auk. Copying and permissions notice: Authorization to copy article content beyond fair use (as specified in Sections 107 and 108 of the U.S. Copyright Law) for internal or personal use, or the internal or personal use of specific clients, is granted by The Regents of the University of California on behalf of the American Ornithologists’ Union for libraries and other users, provided that they are registered with and pay the specified fee through the Copyright Clearance Center (CCC), www.copyright.com. To reach the CCC’s Customer Service Department, phone 978-750-8400 or write to info@copyright. com. For permission to distribute electronically, republish, resell, or repurpose material, and to purchase article offprints, use the CCC’s Rightslink service, available on Caliber at http://caliber. ucpress.net. Submit all other permissions and licensing inquiries through University of California Press’s Rights and Permissions website, www.ucpressjournals.com/reprintInfo.asp, or via e-mail: [email protected]. Back issues of Ornithological Monographs from earlier than 2007 are available from Buteo Books at http://www.buteobooks.com. Issues from 2008 forward are available from University of California Press at http://www.ucpressjournals.com. For complete abstracting and indexing coverage for Ornithological Monographs, please visit http://www.ucpressjournals.com. Library of Congress Control Number 2009923609 ISBN: 978-0-943610-85-6 Issued 30 April 2009 Ornithological Monographs, No. 66 viii + 78 pp. Cover: If core maniraptoran theropod dinosaurs (Dromaeosauridae, Troodontidae, and Oviratorosauria) were actually flightless and flying birds that were more derived towards modern birds than Archaeopteryx, then the hypothesis that birds are maniraptoran theropod dinosaurs would lose most of its current support, and the origin of birds would have to be evaluated in the light of at least four other hypotheses (see Fig. 3 on page 6). Printed by Allen Press on Forest Stewardship Council–certified paper. © 2009 American Ornithologists’ Union. All rights reserved. OM66_FM.indd 2 3/31/09 4:56:50 PM Cladistics and the Origin of Birds: A Review and Two New Analyses by Frances C. James1 and John A. Pourtless IV2 1Department of Biological Science, Florida State University, Tallahassee, Florida 32306, USA; and 21327 High Road #K-1, Tallahassee, Florida 32304, USA ORNITHOLOGICAL MONOGRAPHS NO. 66 PUBLISHED BY THE AMERICAN ORNITHOLOGISTS’ UNION WASHINGTON, D.C. 2009 OM66_FM.indd 3 3/31/09 4:56:51 PM TABLE OF CONTENTS List of tables and figures. vi ABSTRACT. 1 INTRODUCTION. 2 Definition of Aves. 4 THE BMT HYPOTHESIS AND ALTERNATIVES . 4 The BMT Hypothesis. 5 The Neoflightless-theropod Hypothesis. 7 The Early-archosaur Hypothesis. 8 The Crocodylomorph Hypothesis . 8 The Hypothesis that Birds Evolved Twice. 11 CLADISTICS. 11 METHODS . 11 Construction of Matrices . 11 Methods of Analysis of the Matrices . 14 RESULTS. 16 Reanalysis of the CNM Matrix . 16 Analysis of the New Matrix . 18 Alternative Analysis of the New Matrix . 23 DISCUSSION . 25 Has the BMT Hypothesis Been Tested?. 25 Unjustifiable assumptions of homology incorporated into data matrices . 25 Inadequate taxon sampling . 25 Insufficiently rigorous application of cladistic methods . 26 Insufficient tests of primary homology statements . 26 Lack of statistical evaluation . 27 Verificationist arguments . 27 Introduction of ad-hoc auxiliary hypotheses . 27 Evaluation of Alternative Hypotheses. 28 Are predictions of the BMT hypothesis supported by our results? . 28 Are some maniraptorans actually birds more derived than Archaeopteryx? . 30 Weakened support for the BMT hypothesis and the neoflightless-theropod hypothesis . 32 Are alternatives to the BMT hypothesis compatible with the evidence? . 35 CONCLUSIONS . 38 ACKNOWLEDGMENTS. 39 LITERATURE CITED. 39 APPENDIX 1: SPECIMENS EXAMINED . 52 APPENDIX 2: CHARACTER LIST FOR 242 CHARACTERS, NOTES, AND REFERENCES. 52 Notes. 61 APPENDIX 3: ANALYSIS OF CHARACTERS IN THE MANUS, CARPUS, AND TARSUS THAT WERE EXCLUDED FROM THE PRIMARY ANALYSIS OF OUR NEW MATRIX . 63 Manus. 63 Carpus. 64 v OM66_FM.indd 5 3/31/09 4:56:51 PM Disappearance of the avian ulnare and development of the pisiform . 65 Homology of the proximal carpals in Maniraptora . 65 Distribution of proximal carpals in nonmaniraptoran theropods . 65 Homology of the radiale within Aves and between birds and theropods . 66 Homology of the semilunate carpal within Aves . 66 Homology of the semilunate carpal within the Theropoda and between theropods and birds . 67 Identification of distal carpals without knowledge of digital identity . 68 Tarsus: Ascending Process of the Astragalus. 68 APPENDIX 4: DATA MATRIX . 69 APPENDIX 5: NOTES ACCOMPANYING MATRIX ON SCORING DECISIONS FOR CERTAIN TAXA . 76 LIST OF TABLES 1. Taxa included in our analysis and the principal references used for coding their characters . 9 2. Statistics from reanalysis of the 46-taxon × 208-character matrix of Clark et al. (2002).... 19 3. Statistics from analysis of our 79-taxon × 221-character matrix with lengths of most-parsimonious trees (MPTs) when certain theropod taxa were constrained to be within Aves as defined here . 23 4. Statistics from analysis of our 79 taxon × 221 character matrix with lengths of most-parsimonious trees (MPTs) when taxa were constrained to match hypotheses for the origin of birds (BMT = birds are maniraptoran theropod dinosaurs) . 23 5. Five predictions of the BMT (birds are maniraptoran theropod dinosaurs) hypothesis ... 29 6. Some of the major potential synapomorphies with birds that support the three major alternative hypotheses for the origin of birds ...................................... 33 LIST OF FIGURES 1. Alternative relationships of birds and selected maniraptorans . 4 2. Generally accepted phylogeny of the Archosauria including the topology of the BMT hypothesis . 5 3. Five major hypotheses for the origin of birds . 6 4. Embryonic chicken wing bud at (A) 5.5 days of development and (B) 7.5 days of development . 13 5. Carpal cartilages in the chicken wing bud at (A) 9.5, (B) 11.5, and (C) 12.5 days of development . 14 6. (A) Distal and proximal tarsals of Albertosaurus, (B) a composite of the London and Berlin specimens of Archaeopteryx, and (C) the Thermopolis specimen of Archaeopteryx . 15 7. A 50% majority-rule summary of 500 bootstrap replicates of most-parsimonious trees calculated from the matrix reported by Clark et al. (2002) . 17 8. As in Figure 7, but pruned to 24 taxa that represent all the major ingroup clades of Clark et al. (2002) . 18 9. A 50% majority-rule summary of 500 bootstrap replicates of most-parsimonious trees calculated from a matrix of 79 taxa including theropods, birds, nontheropod dinosaurs, and other archosaurs, pruned to 20 taxa . 20 10. As in Figure 9, but with Longisquama also pruned away . 20 vi OM66_FM.indd 6 3/31/09 4:56:51 PM 11. As in Figure 9, pruned to 35 taxa from 79, representing all major proposed sister groups of birds . 21 12. As in Figure 11, but with the Maniraptora pruned away . 22 13. As in Figure 12, but with both maniraptorans and Longisquama pruned away . 22 14. A 50% majority-rule summary of 500 bootstrap replicates of most-parsimonious trees calculated from an alternative analysis to the analyses reported in Figures 9–13, using 242 instead of 221 characters, and pruned as in Figure 11 . 24 15. Skull of Longisquama insignis as preserved on the counterslab of the type specimen (left) and a reconstruction and interpretation of the cranial osteology (right) ................ 37 vii OM66_FM.indd 7 3/31/09 4:56:51 PM Ornithological Monographs Volume (2009), No. 66, 1–78 © The American Ornithologists’ Union, 2009. Printed in USA. CLADISTICS AND THE ORIGIN OF BIRDS: A REVIEW AND TWO NEW ANALYSES Frances C. James1,3 and John A. Pourtless IV2 1Department of Biological Science, Florida State University, Tallahassee, Florida 32306, USA; and 21327 High Road, no. K-1, Tallahassee, Florida 32304, USA Abstract.—The hypothesis that birds are maniraptoran theropod dinosaurs (the “BMT hypo­ thesis”) has become widely accepted by both scientists and the general public. Criticism has usu­ ally been dismissed, often with the comment that no more parsimonious alternative has been presented with cladistic methodology. Rather than taking that position, we ask here whether the hypothesis is as overwhelmingly supported as some claim. We reanalyzed a standard matrix of 46 taxa and 208 characters from a recent paper by Clark, Norell, and Makovicky, and we found statistical support for the clades Coelurosauria and Maniraptoriformes and for a clade of birds and maniraptorans. Note, however, that because the matrix contains only birds and theropods, it assumes that the origin of birds lies within the Theropoda. In addition to this problem, Clark et al.’s (2002) matrix contains problematic assumptions of homology, especially in the palate, basipterygoid, manus, carpus, and tarsus. In an attempt to avoid these two major problems and to evaluate the BMT hypothesis and four alternative hypotheses in a comparative phylogenetic framework, we followed the recommendations of Jenner, Kearney, and Rieppel by constructing and analyzing a larger but more conservative matrix. Our matrix includes taxa from throughout the Archosauria. When the ambiguous characters were excluded, parsimony analyses with boot­ strapping and successive pruning retrieved a weak clade of birds and core maniraptorans (ovirap­ torosaurs, troodontids, and dromaeosaurs) that also contained the early archosaur Longisquama and was not unambiguously associated with other theropods.
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